GSM7839544: 105096-001-034R; Mus musculus; RNA-Seq
Total RNA was isolated using the RNA purification kit NucleoSpin RNA (Macherey-Nagel 740955, Germany) according to the manufacturer's guide. Cells were lysed by adding a mixture of buffer RA1 and dithiothreitol (Sigma-Aldrich, 3483-12-3). The yield of the isolated RNA was then measured using the NanoDrop 1000 spectrophotometer. RNA-seq was conducted using the Illumina NovaSeq 6000 sequencer by GenomeScan (https://www.genomescan.nl/). The procedure included data quality control, adapter trimming, alignment of short reads and feature counting. Library preparation was checked by calculating ribosomal (and globin) content. Checks for possible sample and barcode contamination were performed and a set of standard quality metrics for the raw dataset was determined using quality control tools (FstQC v0.34 and FastQA). Prior to alignment, the reads were trimmed for adapter sequences using Trimmomatic v0.30. To align the reads of each sample, the the  mouse reference GRCm39 was used. Data was analyzed with DESEQ2 in R studio